-
1
-
-
33746377894
-
Protein misfolding, functional amyloid, and human disease
-
Chiti F, Dobson, CM (2006) Protein misfolding, functional amyloid, and human disease. Annu Rev Biochem 75:333-366.
-
(2006)
Annu Rev Biochem
, vol.75
, pp. 333-366
-
-
Chiti, F.1
Dobson, C.M.2
-
3
-
-
77957180065
-
A peculiar form of peripheral neuropathy. Familial atypical generalized amyloidosis with special involvement of peripheral nerves
-
Andrade C (1952) A peculiar form of peripheral neuropathy. Familial atypical generalized amyloidosis with special involvement of peripheral nerves. Brain 75: 408-427.
-
(1952)
Brain
, vol.75
, pp. 408-427
-
-
Andrade, C.1
-
4
-
-
0010551538
-
Amyloid fibril protein related to prealbumin in familial amyloidotic polyneuropathy
-
Costa PP, Figueira AS, Bravo SR (1978) Amyloid fibril protein related to prealbumin in familial amyloidotic polyneuropathy. Proc Natl Acad Sci USA 75:4499-4503.
-
(1978)
Proc Natl Acad Sci USA
, vol.75
, pp. 4499-4503
-
-
Costa, P.P.1
Figueira, A.S.2
Bravo, S.R.3
-
6
-
-
0026612659
-
Transthyretin Pro55, a variant associated with early-onset, aggressive, diffuse amyloidosis with cardiac and neurologic involvement
-
Jacobson DR, McFarlin DE, Kane I, Buxbaum, JN (1992) Transthyretin Pro55, a variant associated with early-onset, aggressive, diffuse amyloidosis with cardiac and neurologic involvement. Hum Genet 89:353-356.
-
(1992)
Hum Genet
, vol.89
, pp. 353-356
-
-
Jacobson, D.R.1
McFarlin, D.E.2
Kane, I.3
Buxbaum, J.N.4
-
7
-
-
0034703380
-
A comparative analysis of 23 structures of the amyloidogenic protein transthyretin
-
Hörnberg A, Eneqvist T, Olofsson A, Lundgren E, Sauer-Eriksson AE (2000) A comparative analysis of 23 structures of the amyloidogenic protein transthyretin. J Mol Biol 302:649-669.
-
(2000)
J Mol Biol
, vol.302
, pp. 649-669
-
-
Hörnberg, A.1
Eneqvist, T.2
Olofsson, A.3
Lundgren, E.4
Sauer-Eriksson, A.E.5
-
8
-
-
0035920156
-
Tetramer dissociation and monomer partial unfolding precedes protofibril formation in amyloidogenic transthyretin variants
-
Quintas A, Vaz DC, Cardoso I, Saraiva MJ, Brito RMM (2001) Tetramer dissociation and monomer partial unfolding precedes protofibril formation in amyloidogenic transthyretin variants. J Biol Chem 276: 27207-27213.
-
(2001)
J Biol Chem
, vol.276
, pp. 27207-27213
-
-
Quintas, A.1
Vaz, D.C.2
Cardoso, I.3
Saraiva, M.J.4
Brito, R.M.M.5
-
9
-
-
0035909981
-
The V122I cardiomyopathy variant of transthyretin increases the velocity of rate-limiting tetramer dissociation, resulting in accelerated amyloidosis
-
Jian X, Buxbaum JN, Kelly JW (2001) The V122I cardiomyopathy variant of transthyretin increases the velocity of rate-limiting tetramer dissociation, resulting in accelerated amyloidosis. Proc Natl Acad Sci USA 98: 14943-14948.
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 14943-14948
-
-
Jian, X.1
Buxbaum, J.N.2
Kelly, J.W.3
-
10
-
-
0030004644
-
The acid-mediated denaturation pathway of transthyretin yields a conformational intermediate that can self-assemble into amyloid
-
Lai Z, Colón W, Kelly JW (1996) The acid-mediated denaturation pathway of transthyretin yields a conformational intermediate that can self-assemble into amyloid. Biochemistry 35:6470-6482.
-
(1996)
Biochemistry
, vol.35
, pp. 6470-6482
-
-
Lai, Z.1
Colón, W.2
Kelly, J.W.3
-
11
-
-
0030694782
-
The amyloidogenic potential of transthyretin variants correlates with their tendency to aggregate in solution
-
Quintas A, Saraiva MJ, Brito RMM (1997) The amyloidogenic potential of transthyretin variants correlates with their tendency to aggregate in solution. FEBS Lett 418:297-300.
-
(1997)
FEBS Lett
, vol.418
, pp. 297-300
-
-
Quintas, A.1
Saraiva, M.J.2
Brito, R.M.M.3
-
12
-
-
0030586945
-
Synchrotron X-ray studies suggest that the core of the transthyretin amyloid fibril is a continuous b-sheet helix
-
Blake C, Serpell L (1996) Synchrotron X-ray studies suggest that the core of the transthyretin amyloid fibril is a continuous b-sheet helix. Structure 4:989-998.
-
(1996)
Structure
, vol.4
, pp. 989-998
-
-
Blake, C.1
Serpell, L.2
-
13
-
-
0031825554
-
From the globular to the fibrous state: Protein structure and structural conversion in amyloid formation
-
Sunde M, Blake CC (1998) From the globular to the fibrous state: protein structure and structural conversion in amyloid formation. Q Rev Biophys 31:1-39.
-
(1998)
Q Rev Biophys
, vol.31
, pp. 1-39
-
-
Sunde, M.1
Blake, C.C.2
-
14
-
-
0033053678
-
Exposure of cryptic epitopes on transthyretin only in amyloid and in amyloidogenic mutants
-
Goldsteins G, Persson H, Andersson K, Olofsson A, Dacklin I, Edvinsson A, Saraiva MJ, Lundgren E (1999) Exposure of cryptic epitopes on transthyretin only in amyloid and in amyloidogenic mutants. Proc Natl Acad Sci USA 96:3108-3113.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 3108-3113
-
-
Goldsteins, G.1
Persson, H.2
Andersson, K.3
Olofsson, A.4
Dacklin, I.5
Edvinsson, A.6
Saraiva, M.J.7
Lundgren, E.8
-
15
-
-
0036784911
-
Arrangement of subunits and ordering of β-strands in an amyloid sheet
-
Serag AA, Altenbach C, Gingery M, Hubbell WL, Yeates TO (2002) Arrangement of subunits and ordering of β-strands in an amyloid sheet. Nat Struct Biol 9: 734-739.
-
(2002)
Nat Struct Biol
, vol.9
, pp. 734-739
-
-
Serag, A.A.1
Altenbach, C.2
Gingery, M.3
Hubbell, W.L.4
Yeates, T.O.5
-
16
-
-
1242316998
-
Probing solvent accessibility of transthyretin amyloid by solution NMR spectroscopy
-
Olofsson A, Ippel JH, Wijmenga SS, Lundgren E, Ohman A (2004) Probing solvent accessibility of transthyretin amyloid by solution NMR spectroscopy. J Biol Chem 279:5699-5707.
-
(2004)
J Biol Chem
, vol.279
, pp. 5699-5707
-
-
Olofsson, A.1
Ippel, J.H.2
Wijmenga, S.S.3
Lundgren, E.4
Ohman, A.5
-
18
-
-
0021525532
-
Characterization of the transition state of lysozyme unfolding. I. Effect of protein-solvent interactions on the transition state
-
Segawa S, Sugihara M (1984) Characterization of the transition state of lysozyme unfolding. I. Effect of protein-solvent interactions on the transition state. Biopolymers 23:2473-2488.
-
(1984)
Biopolymers
, vol.23
, pp. 2473-2488
-
-
Segawa, S.1
Sugihara, M.2
-
19
-
-
0026751786
-
The folding of hen lysozyme involves partially structured intermediates and multiple pathways
-
Radford SE, Dobson CM, Evans PA (1992) The folding of hen lysozyme involves partially structured intermediates and multiple pathways. Nature 358:302-307.
-
(1992)
Nature
, vol.358
, pp. 302-307
-
-
Radford, S.E.1
Dobson, C.M.2
Evans, P.A.3
-
20
-
-
0028227296
-
Tertiary interactions in the folding pathway of hen lysozyme: Kinetic studies using fluorescent probes
-
Itzhaki LS, Evans PA, Dobson CM, Radford SE (1994) Tertiary interactions in the folding pathway of hen lysozyme: kinetic studies using fluorescent probes. Biochemistry 33:5212-5220.
-
(1994)
Biochemistry
, vol.33
, pp. 5212-5220
-
-
Itzhaki, L.S.1
Evans, P.A.2
Dobson, C.M.3
Radford, S.E.4
-
21
-
-
0343632363
-
Submillisecond kinetics of protein folding
-
Eaton WA, Munoz V, Thompson PA, Chan, CK, Hofrichter J (1997) Submillisecond kinetics of protein folding. Curr Opin Struct Biol 7:10-14.
-
(1997)
Curr Opin Struct Biol
, vol.7
, pp. 10-14
-
-
Eaton, W.A.1
Munoz, V.2
Thompson, P.A.3
Chan, C.K.4
Hofrichter, J.5
-
22
-
-
0031055942
-
Kinetic role of early intermediates in protein folding
-
Roder H, Colon W (1997) Kinetic role of early intermediates in protein folding. Curr Opin Struct Biol 7: 15-28.
-
(1997)
Curr Opin Struct Biol
, vol.7
, pp. 15-28
-
-
Roder, H.1
Colon, W.2
-
23
-
-
0028264860
-
Molecular dynamics simulation of protein denaturation: Solvation of the hydrophobic cores and secondary structure of barnase
-
Caflisch A, Karplus M (1994) Molecular dynamics simulation of protein denaturation: solvation of the hydrophobic cores and secondary structure of barnase. Proc Natl Acad Sci USA 91:1746-1750.
-
(1994)
Proc Natl Acad Sci USA
, vol.91
, pp. 1746-1750
-
-
Caflisch, A.1
Karplus, M.2
-
24
-
-
0029124153
-
Acid and thermal denaturation of barnase investigated by molecular dynamics simulations
-
Caflisch A, Karplus M (1995) Acid and thermal denaturation of barnase investigated by molecular dynamics simulations. J Mol Biol 252:672-708.
-
(1995)
J Mol Biol
, vol.252
, pp. 672-708
-
-
Caflisch, A.1
Karplus, M.2
-
25
-
-
0028926875
-
Computational approaches to study protein unfolding: Hen egg white lysozyme as a case study
-
Hunenberger PH, Mark AE, van Gunsteren WF (1995) Computational approaches to study protein unfolding: hen egg white lysozyme as a case study. Proteins 21: 196-213.
-
(1995)
Proteins
, vol.21
, pp. 196-213
-
-
Hunenberger, P.H.1
Mark, A.E.2
van Gunsteren, W.F.3
-
26
-
-
0029963345
-
Identification and characterization of the unfolding transition state of chymotrypsin inhibitor 2 by molecular dynamics simulations
-
Li A, Daggett V (1996) Identification and characterization of the unfolding transition state of chymotrypsin inhibitor 2 by molecular dynamics simulations. J Mol Biol 257:412-429.
-
(1996)
J Mol Biol
, vol.257
, pp. 412-429
-
-
Li, A.1
Daggett, V.2
-
28
-
-
0030775114
-
Can protein unfolding simulate protein folding?
-
Finkelstein AV (1997) Can protein unfolding simulate protein folding? Protein Eng 10::843-845.
-
(1997)
Protein Eng
, vol.10
, pp. 843-845
-
-
Finkelstein, A.V.1
-
29
-
-
0342980331
-
Characterization of the unfolding pathway of the cell-cycle protein p13suc1 by molecular dynamics simulations: Implications for domain swapping
-
Alonso DO, Alm E, Daggett V (2000) Characterization of the unfolding pathway of the cell-cycle protein p13suc1 by molecular dynamics simulations: implications for domain swapping. Structure 8:101-110.
-
(2000)
Structure
, vol.8
, pp. 101-110
-
-
Alonso, D.O.1
Alm, E.2
Daggett, V.3
-
30
-
-
30344487995
-
-
Rodrigues JR, Brito RMM, How important is the role of compact denatured states on amyloid formation by transthyretin? In: Grateau G, Kyle RA, Skinner M, Eds. (2004) Amyloid and Amyloidosis. CRC Press, pp 323-325.
-
Rodrigues JR, Brito RMM, How important is the role of compact denatured states on amyloid formation by transthyretin? In: Grateau G, Kyle RA, Skinner M, Eds. (2004) Amyloid and Amyloidosis. CRC Press, pp 323-325.
-
-
-
-
31
-
-
0037907526
-
Why is Leu55→Pro55 transthyretin variant the most amyloidogenic: Insights from molecular dynamics simulations of transthyretin monomers
-
Yang M, Lei M, Huo S, (2003) Why is Leu55→Pro55 transthyretin variant the most amyloidogenic: insights from molecular dynamics simulations of transthyretin monomers. Protein Sci 12:1222-1231.
-
(2003)
Protein Sci
, vol.12
, pp. 1222-1231
-
-
Yang, M.1
Lei, M.2
Huo, S.3
-
32
-
-
4143067019
-
Pauling and Corey's alpha-pleated sheet structure may define the prefibrillar amyloidogenic intermediate in amyloid disease
-
Armen RS, DeMarco ML, Alonso DO, Daggett V (2004) Pauling and Corey's alpha-pleated sheet structure may define the prefibrillar amyloidogenic intermediate in amyloid disease. Proc Natl Acad Sci USA 101: 11622-11627.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 11622-11627
-
-
Armen, R.S.1
DeMarco, M.L.2
Alonso, D.O.3
Daggett, V.4
-
33
-
-
4644296906
-
Anatomy of an amyloidogenic intermediate: Conversion of betasheet to alpha-sheet structure in transthyretin at acidic pH
-
Armen RS, Alonso DO, Daggett V (2004) Anatomy of an amyloidogenic intermediate: conversion of betasheet to alpha-sheet structure in transthyretin at acidic pH. Structure 12:1847-1863.
-
(2004)
Structure
, vol.12
, pp. 1847-1863
-
-
Armen, R.S.1
Alonso, D.O.2
Daggett, V.3
-
34
-
-
33749325449
-
The sequence-dependent unfolding pathway plays a critical role in the amyloidogenicity of transthyretin
-
Yang M, Yordanov B, Levy Y, Brüschweiler R, Huo S (2006) The sequence-dependent unfolding pathway plays a critical role in the amyloidogenicity of transthyretin. Biochemistry 45:11992-12002.
-
(2006)
Biochemistry
, vol.45
, pp. 11992-12002
-
-
Yang, M.1
Yordanov, B.2
Levy, Y.3
Brüschweiler, R.4
Huo, S.5
-
35
-
-
0033516512
-
Analysis methods for comparison of multiple molecular dynamics trajectories: Applications to protein unfolding pathways and denatured ensembles
-
Kazmirski SL, Li A, Daggett V (1999) Analysis methods for comparison of multiple molecular dynamics trajectories: applications to protein unfolding pathways and denatured ensembles. J Mol Biol 290:283-304.
-
(1999)
J Mol Biol
, vol.290
, pp. 283-304
-
-
Kazmirski, S.L.1
Li, A.2
Daggett, V.3
-
36
-
-
0027476367
-
The x-ray crystal structure refinements of normal human transthyretin and the amyloidogenic Val-30→Met variant to 1.7-Å resolution
-
Hamilton JA, Steinrauf LK, Braden BC, Liepnieks J, Benson MD, Holmgren G, Sandgren O, Steen L (1993) The x-ray crystal structure refinements of normal human transthyretin and the amyloidogenic Val-30→Met variant to 1.7-Å resolution. J Biol Chem 268: 2416-2424.
-
(1993)
J Biol Chem
, vol.268
, pp. 2416-2424
-
-
Hamilton, J.A.1
Steinrauf, L.K.2
Braden, B.C.3
Liepnieks, J.4
Benson, M.D.5
Holmgren, G.6
Sandgren, O.7
Steen, L.8
-
37
-
-
0029092698
-
Fluctuation and cross-correlation analysis of protein motions observed in nanosecond molecular dynamics simulations
-
Hunenberger PH, Mark AE, van Gunsteren WF (1995) Fluctuation and cross-correlation analysis of protein motions observed in nanosecond molecular dynamics simulations. J Mol Biol 252:492-503.
-
(1995)
J Mol Biol
, vol.252
, pp. 492-503
-
-
Hunenberger, P.H.1
Mark, A.E.2
van Gunsteren, W.F.3
-
38
-
-
0001349174
-
Validation of molecular dynamics
-
van Gunsteren WF, Mark AE (1998) Validation of molecular dynamics. J Chem Phys 108:6109-6116.
-
(1998)
J Chem Phys
, vol.108
, pp. 6109-6116
-
-
van Gunsteren, W.F.1
Mark, A.E.2
-
39
-
-
23944524534
-
Data clustering in life sciences
-
Zhao Y, Karypis G (2005) Data clustering in life sciences. Mol Biotechnol 31:55-80.
-
(2005)
Mol Biotechnol
, vol.31
, pp. 55-80
-
-
Zhao, Y.1
Karypis, G.2
-
40
-
-
26444608613
-
Ensemble versus single-molecule protein unfolding
-
Day R, Daggett V (2005) Ensemble versus single-molecule protein unfolding. Proc Natl Acad Sci USA 102: 13445-13450.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 13445-13450
-
-
Day, R.1
Daggett, V.2
-
41
-
-
0037058942
-
Sequence-dependent denaturation energetics: A major determinant in amyloid disease diversity
-
Hammarström P, Jiang X, Hurshman AR, Powers ET, Kelly JW (2002) Sequence-dependent denaturation energetics: a major determinant in amyloid disease diversity. Proc Natl Acad Sci USA 99:16427-16432.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 16427-16432
-
-
Hammarström, P.1
Jiang, X.2
Hurshman, A.R.3
Powers, E.T.4
Kelly, J.W.5
-
42
-
-
0032968133
-
Implicit solvent models
-
Roux B, Simonson T (1999) Implicit solvent models. Biophys Chem 78:1-20.
-
(1999)
Biophys Chem
, vol.78
, pp. 1-20
-
-
Roux, B.1
Simonson, T.2
-
43
-
-
0036306257
-
Native state hydrogen exchange study of suppressor and pathogenic variants of transthyretin
-
Liu K, Kelly JW, Wemmer DE (2002) Native state hydrogen exchange study of suppressor and pathogenic variants of transthyretin. J Mol Biol 320:821-832.
-
(2002)
J Mol Biol
, vol.320
, pp. 821-832
-
-
Liu, K.1
Kelly, J.W.2
Wemmer, D.E.3
-
44
-
-
0033813424
-
A glimpse of a possible amyloidogenic intermediate of transthyretin
-
Liu K, Cho HS, Lashuel HA, Kelly JW, Wemmer DE (2000) A glimpse of a possible amyloidogenic intermediate of transthyretin. Nat Struct Biol 7:754-757.
-
(2000)
Nat Struct Biol
, vol.7
, pp. 754-757
-
-
Liu, K.1
Cho, H.S.2
Lashuel, H.A.3
Kelly, J.W.4
Wemmer, D.E.5
-
45
-
-
0034602241
-
Deuterium-proton exchange on the native wild-type transthyretin tetramer identifies the stable core of the individual subunits and indicates mobility at the subunit interface
-
Liu K, Cho HS, Hoyt DW, Nguyen TN, Olds P, Kelly JW, Wemmer DE (2000) Deuterium-proton exchange on the native wild-type transthyretin tetramer identifies the stable core of the individual subunits and indicates mobility at the subunit interface. J Mol Biol 303: 555-565.
-
(2000)
J Mol Biol
, vol.303
, pp. 555-565
-
-
Liu, K.1
Cho, H.S.2
Hoyt, D.W.3
Nguyen, T.N.4
Olds, P.5
Kelly, J.W.6
Wemmer, D.E.7
-
46
-
-
0037022563
-
Natural β-sheet proteins use negative design to avoid edge-to-edge aggregation
-
Richardson JS, Richardson DC (2002) Natural β-sheet proteins use negative design to avoid edge-to-edge aggregation. Proc Natl Acad Sci USA 99:2754-2759.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 2754-2759
-
-
Richardson, J.S.1
Richardson, D.C.2
-
47
-
-
0030934379
-
Responsive gels formed by the spontaneous self-assembly of peptides into polymeric b-sheet tapes
-
Aggeli A, Bell M, Boden N, Keen JN, Knowles PF, McLeish TC, Pitkeathly M, Radford SE (1997) Responsive gels formed by the spontaneous self-assembly of peptides into polymeric b-sheet tapes. Nature 386: 259-262.
-
(1997)
Nature
, vol.386
, pp. 259-262
-
-
Aggeli, A.1
Bell, M.2
Boden, N.3
Keen, J.N.4
Knowles, P.F.5
McLeish, T.C.6
Pitkeathly, M.7
Radford, S.E.8
-
48
-
-
0036135139
-
A possible role for Π-stacking in the selfassembly of amyloid fibrils
-
Gazit E (2002) A possible role for Π-stacking in the selfassembly of amyloid fibrils. FASEB J 16:77-83.
-
(2002)
FASEB J
, vol.16
, pp. 77-83
-
-
Gazit, E.1
-
49
-
-
17844362202
-
Molecular dynamics simulation of the aggregation of the core-recognition motif of the islet amyloid polypeptide in explicit water
-
Colombo G, Daidone I, Gazit E, Amadei A, Di Nola A (2005) Molecular dynamics simulation of the aggregation of the core-recognition motif of the islet amyloid polypeptide in explicit water. Proteins 59:519-527.
-
(2005)
Proteins
, vol.59
, pp. 519-527
-
-
Colombo, G.1
Daidone, I.2
Gazit, E.3
Amadei, A.4
Di Nola, A.5
-
50
-
-
28244458451
-
Mechanisms of amyloid fibril self-assembly and inhibition: Model short peptides as a key research tool
-
Gazit E (2005) Mechanisms of amyloid fibril self-assembly and inhibition: Model short peptides as a key research tool. FEBS J 272:5971-5978.
-
(2005)
FEBS J
, vol.272
, pp. 5971-5978
-
-
Gazit, E.1
-
51
-
-
0027332116
-
Conversion of α-helices into β-sheets features in the formation of the scrapie prion proteins
-
Pan KM, Baldwin M, Nguyen J, Gasset M, Serban A, Groth D, Mehlhorn I, Huang Z, Fletterick RJ, Cohen FE, Prusiner SB (1993) Conversion of α-helices into β-sheets features in the formation of the scrapie prion proteins. Proc Natl Acad Sci USA 90:10962-10966.
-
(1993)
Proc Natl Acad Sci USA
, vol.90
, pp. 10962-10966
-
-
Pan, K.M.1
Baldwin, M.2
Nguyen, J.3
Gasset, M.4
Serban, A.5
Groth, D.6
Mehlhorn, I.7
Huang, Z.8
Fletterick, R.J.9
Cohen, F.E.10
Prusiner, S.B.11
-
52
-
-
0032544408
-
The crystal structure of amyloidogenic Leu55→Pro transthyretin variant reveals a possible pathway for transthyretin polymerization into amyloid fibrils
-
Sebastião MP, Saraiva MJ, Damas AM (1998) The crystal structure of amyloidogenic Leu55→Pro transthyretin variant reveals a possible pathway for transthyretin polymerization into amyloid fibrils. J Biol Chem 273:24715-24722.
-
(1998)
J Biol Chem
, vol.273
, pp. 24715-24722
-
-
Sebastião, M.P.1
Saraiva, M.J.2
Damas, A.M.3
-
54
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kale L, Schulten K (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26:1781-1802.
-
(2005)
J Comput Chem
, vol.26
, pp. 1781-1802
-
-
Phillips, J.C.1
Braun, R.2
Wang, W.3
Gumbart, J.4
Tajkhorshid, E.5
Villa, E.6
Chipot, C.7
Skeel, R.D.8
Kale, L.9
Schulten, K.10
-
55
-
-
0242593434
-
Development and current status of the CHARMM force field for nucleic acids
-
MacKerell AD Jr, Banavali N, Foloppe N (2001) Development and current status of the CHARMM force field for nucleic acids. Biopolymers 56:257-265.
-
(2001)
Biopolymers
, vol.56
, pp. 257-265
-
-
MacKerell Jr, A.D.1
Banavali, N.2
Foloppe, N.3
-
56
-
-
0029937870
-
Hydrophilicity of cavities in proteins
-
Zhang L, Hermans J (1996) Hydrophilicity of cavities in proteins. Proteins 24:433-438.
-
(1996)
Proteins
, vol.24
, pp. 433-438
-
-
Zhang, L.1
Hermans, J.2
-
57
-
-
0029878720
-
-
Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14:33-38, 27-81.
-
Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14:33-38, 27-81.
-
-
-
-
58
-
-
36749117884
-
Revised TIPS for simulations of liquid water and aqueous solutions
-
Jorgensen WL (1982) Revised TIPS for simulations of liquid water and aqueous solutions. J Chem Phys 77: 4156-4163.
-
(1982)
J Chem Phys
, vol.77
, pp. 4156-4163
-
-
Jorgensen, W.L.1
-
59
-
-
0030059225
-
Ligand binding: Molecular mechanics calculation of the streptavidin-biotin rupture force
-
Grubmuller H, Heymann B, Tavan P (1996) Ligand binding: molecular mechanics calculation of the streptavidin-biotin rupture force. Science 271:997-999.
-
(1996)
Science
, vol.271
, pp. 997-999
-
-
Grubmuller, H.1
Heymann, B.2
Tavan, P.3
-
60
-
-
36449007836
-
Constant pressure molecular dynamics simulation: The Langevin piston method
-
Feller SE, Zhang Y, Pastor RW, Brooks BR (1995) Constant pressure molecular dynamics simulation: the Langevin piston method. J Chem Phys 103:4613-4621.
-
(1995)
J Chem Phys
, vol.103
, pp. 4613-4621
-
-
Feller, S.E.1
Zhang, Y.2
Pastor, R.W.3
Brooks, B.R.4
-
61
-
-
33846823909
-
Particle mesh Ewald. An N. log (N) method for Ewald sums in large systems
-
Darden T, York D, Pedersen L (1993) Particle mesh Ewald. An N. log (N) method for Ewald sums in large systems. J Chem Phys 98:10089-10092.
-
(1993)
J Chem Phys
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
62
-
-
33645310406
-
Assessing the influence of electrostatic schemes on molecular dynamics simulations of secondary structure forming peptides
-
Monticelli L, Simões C, Belvisi L, Colombo, G. (2006) Assessing the influence of electrostatic schemes on molecular dynamics simulations of secondary structure forming peptides. J Phys: Condens Matter 18: S329-S345.
-
(2006)
J Phys: Condens Matter
, vol.18
-
-
Monticelli, L.1
Simões, C.2
Belvisi, L.3
Colombo, G.4
-
63
-
-
33646940952
-
Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of nalkanes
-
Ryckaert JP, Ciccotti G, Berendsen HJC (1977) Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of nalkanes. J Comput Phys 23:327-341.
-
(1977)
J Comput Phys
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
64
-
-
0004014257
-
-
computer program. Department Biochemistry and Molecular Biology, University College, London
-
Hubbard SJ, Thornton JM (1993) 'NACCESS', computer program. Department Biochemistry and Molecular Biology, University College, London.
-
(1993)
NACCESS
-
-
Hubbard, S.J.1
Thornton, J.M.2
-
65
-
-
0029619259
-
Knowledge-based protein secondary structure assignment
-
Frishman D, Argos P (1995) Knowledge-based protein secondary structure assignment. Proteins 23:566-579.
-
(1995)
Proteins
, vol.23
, pp. 566-579
-
-
Frishman, D.1
Argos, P.2
-
66
-
-
0038163983
-
-
Department of Computer Science and Engineering, University of Minnesota, Minneapolis
-
Karypis G (2003) CLUTO - A clustering toolkit. Department of Computer Science and Engineering, University of Minnesota, Minneapolis.
-
(2003)
CLUTO - A clustering toolkit
-
-
Karypis, G.1
|